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Faculty of Health Sciences

Kalan Lab

Publications

Expandable List

Alas, I., Braun, D. R., Ericksen, S. S., Salamzade, R., Kalan, L., Rajski, S. R., & Bugni, T. S. (2024). Micromonosporaceae biosynthetic gene cluster diversity highlights the need for broad-spectrum investigations. Microbial Genomics, 10(1), 001167. https://doi.org/10.1099/mgen.0.001167

De La Cruz, K. F., Townsend, E. C., Alex Cheong, J. Z., Salamzade, R., Liu, A., Sandstrom, S., Davila, E., Huang, L., Xu, K. H., Wu, S. Y., Meudt, J. J., Shanmuganayagam, D., Gibson, A. L. F., & Kalan, L. R. (2024). The porcine skin microbiome exhibits broad fungal antagonism. Fungal Genetics and Biology, 173, 103898. https://doi.org/10.1016/j.fgb.2024.103898

Lane Starr, N. M., Al-Rayyan, N., Smith, J. M., Sandstrom, S., Swaney, M. H., Salamzade, R., Steidl, O., Kalan, L. R., & Singh, A. M. (2024). Combined metagenomic- and culture-based approaches to investigate bacterial strain–level associations with medication-controlled mild-moderate atopic dermatitis. Journal of Allergy and Clinical Immunology: Global, 3(3), 100259. https://doi.org/10.1016/j.jacig.2024.100259

Liu, A., Cheong, J. Z. A., Hassan, S., Wielgat, M. B., Meudt, J. J., Townsend, E. C., Shanmuganayagam, D., Kalan, L. R., & Gibson, A. (2024). The effect of anatomic location on porcine models of burn injury and wound healing. Wound Repair and Regeneration, 32(5), 675–685. https://doi.org/10.1111/wrr.13190

Salamzade, R., Tran, P. Q., Martin, C., Manson, A. L., Gilmore, M. S., Earl, A. M., Anantharaman, K., & Kalan, L. R. (2024). zol & fai: Large-scale targeted detection and evolutionary investigation of gene clusters (p. 2023.06.07.544063). bioRxiv. https://doi.org/10.1101/2023.06.07.544063

Sande, C., Boston, Z. J., Kalan, L. R., & Brennan, M. B. (2023). Next Steps: Studying Diabetic Foot Infections with Next-Generation Molecular Assays. Current Infectious Disease Reports, 25(12), 323–330. https://doi.org/10.1007/s11908-023-00822-8

Spurgeon, M. E., Townsend, E. C., Blaine-Sauer, S., McGregor, S. M., Horswill, M., den Boon, J. A., Ahlquist, P., Kalan, L., & Lambert, P. F. (2024). Key aspects of papillomavirus infection influence the host cervicovaginal microbiome in a preclinical murine papillomavirus (MmuPV1) infection model. mBio, 15(6), e00933-24. https://doi.org/10.1128/mbio.00933-24

Swaney, M. H., Henriquez, N., Campbell, T., Handelsman, J., & Kalan, L. R. (2024). Skin-associated Corynebacterium amycolatum shares cobamides. bioRxiv, 2024.04.28.591522. https://doi.org/10.1101/2024.04.28.591522

Swaney, M. H., Steidl, O. R., Tackett, A., Fye, S., Lee, K. E., Ong, I. M., Bendixsen, C., Spicer, G., DeLine, J., Gern, J. E., Lucey, J., Seroogy, C. M., Kalan, L., & Singh, A. M. (2024). Farm exposure is associated with human breast milk immune profile and microbiome (p. 2024.10.14.618271). bioRxiv. https://doi.org/10.1101/2024.10.14.618271

Townsend, E. C., Cheong, J. Z. A., Radzietza, M., Fritz, B., Malone, M., Bjarnsholt, T., Ousey, K., Swanson, T., Schultz, G., Gibson, A. L. F., & Kalan, L. R. (2024). What is slough? Defining the proteomic and microbial composition of slough and its implications for wound healing. Wound Repair and Regeneration, n/a(n/a). https://doi.org/10.1111/wrr.13170

Townsend, E. C., Xu, K., Cruz, K. D. L., Huang, L., Sandstrom, S., Arend, D., Gromek, O., Scarborough, J., Huttenlocher, A., Gibson, A. L. F., & Kalan, L. R. (2024). Still Not Sterile: Chlorhexidine gluconate treatment does not completely reduce skin microbial bioburden and promotes pathogen overabundance in patients undergoing elective surgeries (p. 2024.07.20.602341). bioRxiv. https://doi.org/10.1101/2024.07.20.602341

Zelasko, S., Swaney, M. H., Sandstrom, S., Davenport, T. C., Seroogy, C. M., Gern, J. E., Kalan, L. R., & Currie, C. R. (2024). Upper respiratory microbial communities of healthy populations are shaped by niche and age. Microbiome, 12, 206. https://doi.org/10.1186/s40168-024-01940-8

Zelasko, S., Swaney, M.-H., Suh, W. S., Sandstrom, S., Carlson, C., Cagnazzo, J., Golfinos, A., Fossen, J., Andes, D., Kalan, L. R., Safdar, N., & Currie, C. R. (2024). Altered oral microbiota of drug-resistant organism carriers exhibit impaired gram-negative pathogen inhibition (p. 2024.09.24.614756). bioRxiv. https://doi.org/10.1101/2024.09.24.614756

Salamzade, R., Cheong, J. Z. A., Sandstrom, S., Swaney, M. H., Stubbendieck, R. M., Starr, N. L., Currie, C. R., Singh, A. M., & Kalan, L. R. (2023). Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC. Microbial Genomics, 9(4), 000988. https://doi.org/10.1099/mgen.0.000988

Salamzade, R., & Kalan, L. R. (2023). skDER: Microbial genome dereplication approaches for comparative and metagenomic applications. bioRxiv, 2023.09.27.559801. https://doi.org/10.1101/2023.09.27.559801

Starr NL, Steidl O, Smith J, Sandstrom S, Swaney MH, Singh AM, Kalan LR (2023) Mild-moderate atopic dermatitis controlled by medication exhibits similar bacterial taxa to controls, but strain-level effects and virome disruption persist. Journal of Allergy and Clinical Immunology 151(2); doi: https://doi.org/10.1016/j.jaci.2022.12.719

Swaney MH, Nelsen A, Kalan, LR (2023) Sweat and Sebum Preferences of the Human Skin Microbiota. Microbiology Spectrum e04180-22; doi: https://doi.org/10.1128/spectrum.04180-22

Townsend EC, Kalan, LR (2023) The dynamic balance of the skin microbiome across the lifespan. Biochemical Society Transactions; doi: https://doi.org/10.1042/BST20220216 (PDF)

Salamzade R, Swaney MH, Kalan LR (2022) Comparative genomic and metagenomic investigations of the Corynebacterium tuberculostearicum species complex reveals potential mechanisms underlying associations to skin health and disease. Clinical Microbiology 11(1); doi: https://doi.org/10.1128/spectrum.03578-22

Nguyen UT, Kalan LR (2022) Forgotten fungi: the importance of the skin mycobiome. Current Opinion in Microbiology 70, 102235; doi: https://doi.org/10.1016/j.mib.2022.102235

Cheong JZA, Liu A, Rust C, Kalan LR, Gibson A (2022) Robbing Peter to pay Paul: Chlorhexidine gluconate demonstrates short-term efficacy and long-term cytotoxicity. Wound Repair and Regeneration 30(5), 573 – 584; doi: https://doi.org/10.1111/wrr.13044

Swaney MH, Sandstrom S, Kalan LR (2022) Cobamide sharing is predicted in the human skin microbiome. mSystems 7(5); doi: https://doi.org/10.1128/msystems.00677-22

Cheong JZA, Irvine JM, Roesemann S, Nora, A, Morgan, CE, Daniele C, Kalan LR, Brennan MB (2022) Ankle brachial indices & anaerobes: Is peripheral vascular disease associated with anaerobic bacteria in diabetic foot ulcers? Therapeutic Advantage in Endocrinology and Metabolism; 13 (1-12) doi: https://doi.org/10.1177/20420188221118747 (PDF)

Salamzade R, Cheong JZA, Sandstrom S, Swaney MH, Stubbendieck RM, Starr NL, Currie CR, Singh AM, Kalan LR (2022) IsaBGC provides a comprehensive framework for evolutionary analysis of biosynthetic gene clusters within focal taxa. bioRxiv. 2022 June; doi: https://doi.org/10.1101/2022.04.20.488953

Kieft K, Adams A, Salamzade R, Kalan L, Anantharaman K (2022) vRhyme enables binning of viral genomes from metagenomes. Nucleic Acids Research 50(14); doi: https://doi.org/10.1093/nar/gkac341 (PDF)

Swaney MH, Kalan LR (2022) Two-for-one: Dual host-microbe functions of S. epidermidis sph. Cell Host & Microbe 30(3); doi: https://doi.org/10.1016/j.chom.2022.02.011

Starr NL, Steidl O, Smith J, Sandstrom S, Swaney MH, Singh AM, Kalan L (2022) Culturing of bacterial isolates from skin of pediatric atopic dermatitis subjects. The Journal of Allergy and Clinical Immunology 149(2); doi: https://doi.org/10.1016/j.jaci.2021.12.445

Steidl O, Starr NL, Smith J, Kalan L, Singh AM (2022) Staphylococcus aureus disruption of keratinocytes in atopic dermatitis. The Journal of Allergy and Clinical Immunology 149(2); doi: https://doi.org/10.1016/j.jaci.2021.12.748

Johnson CJ, Cheong JZA, Shanmuganayagam D, Kalan LR, Nett JE (2022) Modeling Candida auris colonization on porcine skin ex vivo. Methods in molecular biology, 251-258; doi: https://doi.org/10.1007/978-1-0716-2417-3_20

Cheong A, Rust C, Liu A, Kalan L, Gibson A (2021) Trade-offs between antiseptic efficacy and cytotoxicity in a human ex vivo wound contamination model. bioRxiv. 2021 May; doi: https://doi.org/10.1101/2021.02.14.430155

Swaney MH, Kalan LR (2021) 197 Investigation of vitamin B12 sharing within the skin microbiome. Journal of Investigative Dermatology 141(5); doi: https://doi.org/10.1016/j.jid.2021.02.218

Cheong JZA, Johnson CJ, Wan H, Liu A, Kernien JF, Gibson ALF, Nett JE, Kalan LR (2021) Priority effects dictate community structure and alter virulence of fungal-bacterial biofilms. The ISME Journal 15, 2012-2027; doi: https://doi.org/10.1038/s41396-021-00901-5

Swaney MH, Kalan LR (2021) Living in your skin: Microbes, molecules, and mechanisms. ASM Infection and Immunity 89(4); doi: 10.1128/IAI.00695-20

Bradley CW, Lee FF, Rankin SC, Kalan LR, Horwinski J, Morris DO, Grice EA, Cain CL (2020) The otic microbiota and mycobiota in a referral population of dogs in eastern USA with otitis externa. Veterinary Dermatology 31(3); doi: doi.org/10.1111/vde.12826

Horton MV, Johnson CJ, Kernien JF, Patel TD, Lam BC, Cheong JZA, Meudt JJ, Shanmuganayagam D, Kalan LR, Nett JE (2020) Candida auris forms high-burden biofilms in skin niche conditions and on porcine skin. mSphere 5(1); doi: https://doi.org/10.1128/mSphere.00910-19

Davis SC, Solis M, Gil J, Higa A, Metzger S, and Kalan L (2019) Effects of topical antimicrobial formulations on Pseudomonas aeruginosa infection in a porcine burn wound model. bioRxiv. 2019 August; doi: https://doi.org/10.1101/737338

Deusenbery CB, Kalan L, Meisel M, Garder SE, Grice E, and Spiller K (2019) Human macrophage response to microbial supernatants from diabetic foot ulcers. Wound Repair and Regeneration 27(6), 598-608; doi: https://doi.org/10.1111/wrr.12752

Kalan LR, Meisel JS, Loesche MA, Horwinski J, Soaita I, Chen X, Uberoi A, Gardner SE, Grice EA (2019) Strain- and species-level variation in the microbiome of diabetic wounds is associated with clinical outcomes and therapeutic efficacy. Cell Host & Microbe 25(5), 641-655; doi: 10.1016/j.chom.2019.03.006

Uberoi A, Campbell A, Kalan L, Lovins V, White E, Gardener S, Grice EA (2019) 940 Epithelial-microbial crosstalk modifies wound healing outcomes: from shotgun metagenomics to mechanistic understanding. Journal of Investigative Dermatology 139(5); doi: https://doi.org/10.1016/j.jid.2019.03.1016

Cheong JZA, and Kalan LR (2019) Wound microbiome update: sequencing and behavior. Wounds International 10(4); https://www.akademie-zwm.ch/uploads/media/konsensusdokumente/Wound_microbiome_update_sequencing_and_behaviour_WOUNDS_2019.pdf (PDF)

Kalan LR, Brennan MB (2018) The role of the microbiome in nonhealing diabetic wounds. Annals of the New York Academy of Sciences 1435(1), 79-92; doi: https://doi.org/10.1111/nyas.13926

Kalan L, Grice EA (2018) Fungi in the wound microbiome. Advances in Wound Care 7(7); doi: https://doi.org/10.1089/wound.2017.0756

Kalan L, Zhou M, Labbie M, Willing B (2017) Measuring the microbiome of chronic wounds with use of a topical antimicrobial dressing – A feasibility study. PLoS ONE; doi: https://doi.org/10.1371/journal.pone.0187728

Kalan LR, Pepin DM, Ul-Haq I, Miller SB, Hay ME, Precht RJ (2017) Targeting biofilms of multidrug-resistant bacteria with silver oxynitrate. International Journal of Antimicrobial Agents 49(6), 719-726; doi: https://doi.org/10.1016/j.ijantimicag.2017.01.019

Lemire JA, Kalan L, Gugala N, Bradu A, Turner RJ (2017) Silver oxynitrate – an efficacious compound for the prevention and eradication of dual-species biofilms. Biofouling 33(6), 460-469; doi: https://doi.org/10.1080/08927014.2017.1322586

Lemire J, Chatfield-Reed K, Kalan L, Gugala N, Westersund, Almblad H, Chua G, Turner RJ (2017) Unravelling the myths and mysteries of the antimicrobial agent, silver. The FASEB Journal; doi: https://doi.org/10.1096/fasebj.31.1_supplement.939.2

Loesche M, Gardner SE, Kalan L, Horwinski J, Zheng Q, Hodkinson BP, Tyldsley AS, Franciscus CL, Killis SL, Mehta S, Margolis DJ, Grice EA (2016) Temporal stability in chronic wound microbiota is associated with poor healing. Journal of Investigative Dermatology 137(1), 237-244; doi: https://doi.org/10.1016/j.jid.2016.08.009

Kalan L, Gardner SE, Grice EA (2016) Reply to “Understanding the Role of Fungi in Chronic Wounds”. MBio 7(6) e02033-16; doi: https://doi.org/10.1128/mBio.02033-16 (PDF)

Kalan L, Loesche M, Hodkinson BP, Heilmann K, Ruthel G, Gardner SE, Grice EA (2016) Redefining the Chronic-Wound Microbiome: Fungal Communities Are Prevalent, Dynamic, and Associated with Delayed Healing. MBio 7(5) 201058-16; doi: https://doi.org/10.1128/mBio.01058-16 (PDF)

Swanson T, Angel D, Sussman G, Cooper R, Haeslet E, Ouset K, Carville K, Fletcher J, Kalan L, Keast D, Leaper DJ, Schultz G, Black J, Call E (2016) Wound infection in clinical practice: principles of best practice. Wounds International. 2016 December;  http://eprints.hud.ac.uk/id/eprint/30637

Zhu XM, Hackl S, Thaker MN, Kalan L, Weber C, Urgast DS, Krupp EM, Brewer A, Vanner S, Szawiola A, Yim G, Feldmann J, Bechthold A, Wright GD, Zechel DL (2015) Biosynthesis of the fluorinated natural product nucleocidin in Streptomyces calvus is dependent on the bldA-specified leu-tRNA(UUA) molecule. ChemBioChem. 2015 November 16(17), 2498-2506; doi: https://doi.org/10.1002/cbic.201500402

Lemire JA, Kalan L, Bradu A, Turner RJ (2015) Silver oxynitrate, an unexplored silver compound with antimicrobial and antibiofilm activity. Antimicrobial Agents and Chemotherapy. 2015 June 33(6), 460-469; doi: https://doi.org/10.1128/AAC.05177-14

Frasch HJ, Kalan L, Kilian R, Martin T, Wright GD, Stegmann E (2015) Alternative pathway to a glycopeptide-resistant cell wall in the balhimycin producer Amycolatopsis balhimycina. ACS Infectious Diseases. 2015 May 1(6), 253-261; doi: https://doi.org/10.1021/acsinfecdis.5b00011

Thaker MN, Kalan L, Waglechner N, Eshaghi A, Patel SN, Poutanen S, Willey B, Coburn B, McGeer A, Low DE, Wright GD (2015) Vancomycin-variable enterococci can give rise to constitutive resistance during antibiotic therapy. Antimicrobial Agents Chemotherapy. 2015 February 59(3); doi: https://doi.org/10.1128/AAC.04490-14

Yim G, Kalan L, Koteva K, Thaker MN, Waglechner N, Tang I, Wright GD (2014) Harnessing the synthetic capabilities of glycopeptide antibiotic tailoring enzymes: characterization of the UK-68,597 biosynthetic cluster. ChemBioChem. 2014 September 15(17), 2613-2623; doi: https://doi.org/10.1002/cbic.201402179

Szakacs TA, Kalan L, McConnell MJ, Eshaghi A, Shahinas D, McGeer A, Wright GD, Low DE, Patel SN (2014) Outbreak of vancomycin-susceptible Enterococcus faecium containing the wild-type vanA gene. Journal of Clinical Microbiology 52(5); doi: https://doi.org/10.1128/JCM.03563-13

Kalan L, Perry J, Koteva K, Thaker M, Wright G (2013) Glycopeptide sulfation evades resistance. Journal of Bacteriology 195(1); doi: https://doi.org/10.1128/JB.01617-12

Kalan L, Gessner A, Thaker MN, Waglechner N, Zhu X, Szawiola A, Bechthold A, Wright GD, Zechel DL (2013) A cryptic polyene biosynthetic gene cluster in Streptomyces calvus is expressed upon complementation with a functional bldA gene. Chemistry & biology 20(10), 1214-1224; doi: https://doi.org/10.1016/j.chembiol.2013.09.006

McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O’Brien JS, Pawlowski AC, Piddock LJ, Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD (2013) The comprehensive antibiotic resistance database. Antimicrobial Agents Chemotherapy 57(7), 3348-3357; doi: 10.1128/AAC.00419-13

Kalan LR (2012) Exploiting glycopeptide tailoring enzymes as an approach to overcome resistance. Open Access Dissertations and Theses. 2012 October; http://hdl.handle.net/11375/12331

Shi R, Munger C, Kalan L, Sulea T, Wright GD, Cygler M (2012) Sulfonation of glycopeptide antibiotics by sulfotransferase StaL depends on conformational flexibility of aglycone scaffold. Proceedings of the National Academy of Sciences 109 (29), 11824-11829; doi: https://doi.org/10.1073/pnas.1205377109

D’Costa VM, King CE, Kalan L, Morar M, Sung WW, Schwarz C, Froese D, Zazula G, Calmels F, Debruyne R, Golding GB, Poinar HN, Wright GD (2011) Antibiotic resistance is ancient. Nature 477, 457-461; doi: https://doi.org/10.1038/nature10388

Kalan L, Wright GD (2011) Antibiotic adjuvants: multicomponent anti-infective strategies. Expert Reviews in Molecular Medicine 13; doi: 10.1017/S1462399410001766

Kalan L, Ebert S, Kelly T, Wright GD (2009) Noncanonical vancomycin resistance cluster from Desulfitobacterium hafniense Y51. Antimicrobial Agents Chemotherapy 53(7); doi: https://doi.org/10.1128/AAC.01408-08